Immunomodulation by altering sphingosine 1-phosphate lyase (spl) activity

ABSTRACT

Compositions and methods for modulating immune function are provided based on the unexpected discovery that inhibition of sphingosine-1-phosphate lyase (SPL) activity confers useful immunosuppressive effects, for example to modulate immune function in treatment or prevention of inflammation, transplant graft rejection, autoimmune disease, allergy, or other conditions, including therapeutic alteration of immune system cell survival and/or proliferation. Altering SPL activity by direct or indirect pharmacological intervention, or alternatively by molecular genetic methods to alter SPL expression levels, are also contemplated.

STATEMENT OF GOVERNMENT INTEREST

This invention was made with government support under Grant No. CA77528 awarded by the National Institutes of Health. The government may have certain rights in this invention.

FIELD OF THE INVENTION

The present invention relates generally to compositions and methods for immune system regulation, and more particularly to therapeutic intervention to modulate immune function by influencing specific metabolic and signal transduction pathways that involve sphingolipids.

BACKGROUND OF THE INVENTION Description of the Related Art

Sphingolipid metabolites and enzymes of sphingolipid metabolism play important roles in regulating cell migration, stress response, survival, differentiation, senescence, apoptosis, receptor signaling, and endocytosis in eukaryotic cells. These findings suggest molecular mechanisms by which sphingolipids may affect animal physiology and contribute to disease states. Mutations that result in failure or dysregulation of sphingolipid synthesis or catabolism are directly responsible for a number of human diseases, including hereditary sensory neuropathy type 1 and the group of lysosomal storage diseases called the sphingolipidoses (Bejaoui et al., 2001 Nat Genet. 27:261-2; Dawkins et al., 2001 Nat Genet. 27:309-12; Gable et al., 2002 J Biol Chem 277, 10194-200).

Sphingosine-1-phosphate (S1P) is an endogenous sphingolipid metabolite present in most mammalian cells and in serum, and is formed by phosphorylation of sphingosine mediated by the cellular enzyme sphingosine kinase (SK). Like other sphingolipid metabolites such as ceramide and sphingosine, S1P participates in specific signal transduction pathways. Many of the effects of S1P signaling, which include promotion of cellular proliferation, enhancement of migration, inhibition of apoptosis and stimulation of angiogenesis, influence the transformation, growth, drug resistance, vascularity and metastatic capacity of cancer cells. Several observations support the notion that sphingosine kinase (SK) and sphingosine-1-phosphate lyase (SPL) may be cancer related genes. First, the overexpression of SK in NIH3T3 fibroblasts leads to oncogenic transformation as determined by the ability of transfected cells to form foci in vitro and to form fibrosarcomas in NOD/SCID mice. Second, human SPL was cloned and mapped to 10q21, a chromosomal region frequently deleted in a variety of human cancers.

As noted above, S1P mediates a variety of cell signaling activities and is believed to do so by interacting specifically with multiple cellular receptors, including a family of G protein-coupled receptors. One such receptor, S1P₁, has been shown to interact with a synthetic prodrug, FTY720, only after phosphorylation of the prodrug by SK yields the drug in its active form, FTY720P.

FTY720 is an immunosuppressive agent that modulates lymphocyte trafficking and prevents allograft rejection (Budde et al., (2002) J Am Soc Nephrol 13, 1073-1083; Brinkmann, V. (2004) Yonsei Med J 45, 991-997). FTY720 treatment stimulates lymphocyte homing to peripheral lymph nodes and Peyer's patches, resulting in prolonged survival of allograft tissues and both prevention and treatment of various autoimmune diseases in animal models (Brinkmann, V., and Lynch, K. R. (2002) Curr Opin Immunol 14, 569-575). FTY720 induces numerous effects on the immune system including inhibited egress of both naïve and activated CD4+, CD8+ and B lymphocytes from peripheral lymphoid organs and thymus, cysteinyl leukotriene-dependent T cell chemotaxis to lymph nodes, peripheral blood lymphopenia, egress of lymphocytes from the spleen, displacement of B cells from the marginal zone of the spleen, decreased β1 integrin expression on marginal zone B cells, homing of hematopoietic progenitor cells to the bone marrow, and decreased vascular permeability (Chiba et al., (1998) J Immunol 160, 5037-5044; Matloubian et al, (2004) Nature 427, 355-360; Mandala et al., (2002) Science 296, 346-349; Xie et al., (2003) J Immunol 170, 3662-3670; Vora et al., (2005) J Leukocyte Biology 78, 1-10; Honig et al., (2003) J Clin Invest 111, 627-637; Sanchez et al., (2003) J Biol Chem 278, 47281-47290; Kimura et al., (2004) Blood ______; Halin et al., (2005) Blood epub ahead of print). Importantly, while FTY720 prevents the migration of lymphocytes to allogeneic graft tissue and other sites of inflammation, it does not diminish the activation, proliferation or effector functions of B and T lymphocytes in response to antigen stimulation (Pinschewer et al., (2000) J Immunol 164, 5761-5770). Toxicities associated with FTY720 are limited and distinct from those of other immunosuppressive drugs, which makes FTY720 a candidate for combination immunosuppressive transplantation regimens.

FTY720 was rationally designed based on chemical modifications of myriocin, a naturally occurring sphingoid base analog that causes immunosuppression by interrupting sphingolipid metabolism (Fujita et al., (1994) J Antibiol (Tokyo) 47, 208-215). FTY720 is phosphorylated in vivo (Billich et al., (2003) J Biol Chem 278, 47408-47415), and as noted above, the phosphorylated form of the drug acts as an agonist for a family of G protein coupled receptors that recognize the sphingolipid metabolite (and SK product) sphingosine 1-phosphate (S1P) as the endogenous ligand (Mandala et al., (2002) Science 296, 346-349; Brinkmann et al., (2002) J Biol Chem 277, 21453-21457). Genetic and biochemical evidence suggests that FTY720P-induced activation of the S1P₁ receptor is primarily responsible for the effect of the drug on lymphocytes (Matloubian et al, (2004) Nature 427, 355-360). While FTY720P is an S1P₁ receptor agonist, exposure to the drug also results in receptor internalization and downregulation on lymphocytes, which is thought to be the mechanism of action, since reconstitution of mice with hematopoietic progenitors or lymphocytes lacking S1P₁ expression emulates the effects of FTY720 treatment on lymphocyte egress and trafficking (Allende et al., (2004) J Biol Chem 279, 15396-15401; Graler et al., (2004) Faseb J 18, 551-553).

Intracellular S1P levels are regulated by SK-mediated synthesis of S1P from sphingosine, and by S1P degradation by lipid phosphatases and by the enzyme SPL, a pyridoxal 5′-phosphate-dependent enzyme that resides in the ER and is responsible for the irreversible degradation of S1P to ethanolamine phosphate and hexadecimal (Spiegel et al., (2000) FEBS Lett 476, 55-57). Given the pleiotropic effects of FTY720 and of SIP, however, there is clearly a need for an improved ability to modulate immune function. As described herein, the present invention addresses this need and offers other related advantages.

BRIEF SUMMARY OF THE INVENTION

According to certain embodiments of the present invention, there is provided a method of modulating immune function in a subject, comprising administering to the subject an agent that alters sphingosine-1-phosphate lyase (SPL) activity, and thereby modulating immune function. In certain further embodiments modulating immune function comprises reducing or preventing tissue inflammation in the subject, and in certain other further embodiments modulating immune function comprises treating or preventing a condition that is selected from transplant graft rejection, autoimmune disease and allergy, and in certain other further embodiments modulating immune function comprises altering proliferation or survival of an immune system cell. In a still further embodiment the immune system cell is a lymphocyte or a hematopoietic cell of lymphoid lineage.

In another embodiment the agent that alters sphingosine-1-phosphate lyase (SPL) activity is capable of decreasing SPL activity, and in a further embodiment the agent that is capable of decreasing SPL activity binds to SPL. In another further embodiment the agent that is capable of decreasing SPL activity causes a decreased expression level of SPL. In another further embodiment the agent that causes a decreased expression level of SPL is selected from (a) an antisense polynucleotide that specifically hybridizes to a nucleic acid molecule that encodes a SPL polypeptide, (b) a ribozyme that specifically cleaves a nucleic acid molecule that encodes a SPL polypeptide, (c) a small interfering RNA that is capable of interfering with a nucleic acid molecule that encodes a SPL polypeptide, (d) an agent that alters activity of a regulatory element that is operably linked to a nucleic acid molecule that encodes a SPL polypeptide, and (e) an antibody that specifically binds to a translated product of a nucleic acid molecule that encodes a SPL polypeptide, wherein the nucleic acid molecule that encodes a SPL polypeptide is selected from (i) a nucleic acid molecule comprising a nucleotide sequence as set forth in SEQ ID NO:1 (nucleic acid encoding human SPL polypeptide) or a complementary sequence thereto, or as set forth in SEQ ID NO:3 (nucleic acid encoding murine SPL polypeptide) or a complementary sequence thereto, (ii) a nucleic acid molecule comprising a nucleotide sequence that hybridizes under moderately stringent conditions to the nucleic acid molecule of (i) and that encodes a polypeptide having sphingosine-1-phosphate lyase (SPL) activity, and (iii) a nucleic acid molecule that encodes a SPL polypeptide which comprises an amino acid sequence as set forth in SEQ ID NO:2 (human SPL) or a portion of SEQ ID NO:2 having sphingosine-1-phosphate lyase (SPL) activity, or as set forth in SEQ ID NO:4 (murine SPL) or a portion of SEQ ID NO:4 having sphingosine-1-phosphate lyase (SPL) activity.

In another embodiment the agent that alters sphingosine-1-phosphate lyase (SPL) activity is not FTY720 or myriocin. In another embodiment the agent that alters sphingosine-1-phosphate lyase (SPL) activity is selected from deoxypyridoxine, C₈-cyclopropenylceramide and C₁₋₆-cyclopropenylceramide. In another embodiment the agent that alters sphingosine-1-phosphate lyase (SPL) activity alters activity of a regulatory element that is operably linked to a nucleic acid molecule that encodes a SPL polypeptide, wherein the regulatory element comprises a GATA transcription factor-binding motif. In another embodiment the agent that alters sphingosine-1-phosphate lyase (SPL) activity is selected from (a) a mutated form of a nucleic acid molecule that encodes a SPL polypeptide wherein the mutated form encodes a dominant negative mutant SPL polypeptide, or a complementary polynucleotide thereto, and (b) a dominant negative mutant SPL polypeptide encoded by (a), wherein the nucleic acid molecule that encodes a SPL polypeptide is selected from the group consisting of (i) a nucleic acid molecule comprising a nucleotide sequence as set forth in SEQ ID NO:1 or a complementary sequence thereto, or as set forth in SEQ ID NO:3 or a complementary sequence thereto, (ii) a nucleic acid molecule comprising a nucleotide sequence that hybridizes under moderately stringent conditions to the nucleic acid molecule of (i) and that encodes a polypeptide having sphingosine-1-phosphate lyase (SPL) activity, and (iii) a nucleic acid molecule that encodes a SPL polypeptide which comprises an amino acid sequence as set forth in SEQ ID NO:2 or a portion of SEQ ID NO:2 having sphingosine-1-phosphate lyase (SPL) activity, or as set forth in SEQ ID NO:4 or a portion of SEQ ID NO:4 having sphingosine-1-phosphate lyase (SPL) activity.

These and other aspects of the present invention will become apparent upon reference to the following detailed description and attached drawings. All references (including websites and including the following patents and patent applications: U.S. Pat. No. 6,423,527; U.S. Pat. No. 6,569,666; U.S. Pat. No. 6,495,359; U.S. application Ser. No. 10/053,510; U.S. application Ser. No. 10/286,175; U.S. application Ser. No. 10/197,073; U.S. application Ser. No. 10/348,052; U.S. application Ser. No. 10/622,011; PCT/US2003/01739) disclosed herein are hereby incorporated by reference in their entireties as if each was incorporated individually.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows stability of FTY720-P in the presence of SPL. (A) Twenty nanomoles of FTY720-P were incubated with SPL enzyme for 0-24 hours under standard SPL reaction conditions in the absence of dihydrosphingosine 1-phosphate substrate. At the indicated times the reaction was stopped, and FTY720-P was recovered and quantified by HPLC. (B) Twenty nanomoles of S1P were incubated with extracts from cells overexpressing SPL for 0-24 hours, or alternatively, with extracts from cells containing pcDNA3.0 vector control which had no appreciable SPL activity (PC) for 2 hours. S1P was recovered and quantified by HPLC.

FIG. 2 shows inhibition of SPL activity by FTY720 in vivo. One mg/kg FTY720 was administered by peritoneal injection to FVB mice at time zero. Mice were euthanized at the indicated times, and SPL activity in thymic tissue was determined.

FIG. 3 shows inhibition of SPL activity by FTY720 in vitro. Various concentrations of FTY720 or its phosphorylated derivative (FTY720P) were incubated for 30 minutes on ice with whole cell extracts containing high SPL activity by virtue of a human SPL adenoviral expression construct. SPL activity was determined. (A) FTY720; (B) FTY720-P.

FIG. 4 shows SPL expression was not affected by FTY720 or FTY720P. (A) SPL gene expression. HEK293 cells were co-transfected with a human SPL luciferase reporter construct and the sea pansy luciferase reporter as a control for transfection efficiency. Twenty-four hours after transfection, cells were treated with 0.3 μM FTY720, 3.0 μM FTY720 or vehicle and incubated for another 24 hours at 37° C. Luciferase activity was then determined as a measure of expression, as described in Experimental Methods. Values shown are luciferase activity normalized to sea pansy luciferase; (B) SPL protein expression. Thymic extracts from control mice (time 0) and mice treated with FTY720 for 24 hours were evaluated for SPL protein expression by immunoblotting. Actin was used as a loading control.

FIG. 5 shows the effects of the SPL inhibitor GT11 (C8-cyclopropenylceramide, Matreya LLC, Pleasant Gap, Pa., catalogue number 1886) on LPS-stimulated proliferation of C3H murine splenocytes and thymocytes in vitro.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to the surprising discovery that altering (i.e., increasing or decreasing in a statistically significant manner) SPL activity results in altered immune function, and thus in its various embodiments provides methods and compositions for modulating (i.e., altering) immune function. Accordingly there is provided, in the form of SPL, a target for therapeutic intervention to modulate immune function in a subject. It will be appreciated that in certain preferred embodiments, alteration of SPL by decreasing SPL activity to modulate immune function, whether by directly or indirectly inhibiting SPL catalytic degradation of S1P, or by substantially impairing (i.e., decreasing in a statistically significant manner) SPL expression levels, desirably influences one or more particular immunological parameters to confer clinical benefits.

As described herein, the unexpected immunomodulatory role of SPL was identified through determination that the immunosuppressive agent FTY720 can directly inhibit SPL activity. As described above, FTY720 was previously believed to exert physiological effects only as a S1P receptor (S1P₁) agonist following its specific conversion by SK to the phosphorylated form of the drug, FTY720P. Hence, only in view of the present application can it be appreciated that pharmacological intervention by way of altering SPL activity results in useful therapeutic modalities to modulate immune function. For example, SPL inhibitors (alone or in combination with other immunomodulatory agents) may usefully promote immune suppression to prevent rejection of solid organ or bone marrow grafts in transplantation medicine, and/or to prevent sequelae of autoimmune diseases.

Immune function is mediated by immune system cells which include, but are not limited to, cells of hematopoietic origin including cells at various stages of differentiation within myeloid and lymphoid lineages and which may (but need not) express one or more types of lineage-specific, subpopulation-specific and/or functional cell surface molecules including well known differentiation markers, as may be found, for instance, on T lymphocytes, B lymphocytes, NK cells, monocytes, macrophages, dendritic cells, neutrophils, basophils, eosinophils, mast cells, erythrocytes, and precursors, progenitors (e.g., hematopoietic stem cells), quiescent, activated and mature forms of such cells. (see, e.g., Leucocyte Typing VII, 2002, Mason et al. (Eds.), Oxford Univ. Press, London) Other immune system cells may include cells of non-hematopoietic origin that are capable of mediating immune functions, for example, endothelial cells, keratinocytes, fibroblasts, osteoclasts, epithelial cells and other cells. Immune system cells may also include cells that mediate cytotoxic or cytostatic events, or endocytic, phagocytic, or pinocytotic events, or that effect induction of apoptosis, or that effect microbial immunity or neutralization of microbial infection, or cells that mediate allergic, inflammatory, hypersensitivity and/or autoimmune reactions. According to certain preferred embodiments described herein, an immune system cell may be a lymphocyte such as a T lymphocyte or a B lymphocyte or another hematopoietic cell of lymphoid lineage.

As will be known to persons having ordinary skill in the art, immune function includes an immune response, which may be any active alteration of the immune status of a host, and which may include any alteration in the structure or function of one or more tissues, organs, cells or molecules that participate in maintenance and/or regulation of host immune status. Typically, immune responses may be detected by any of a variety of well known parameters, including but not limited to in vivo or in vitro determination of: soluble immunoglobulins or antibodies; soluble mediators such as cytokines, lymphokines, chemokines, hormones, growth factors and the like as well as other soluble small peptide, carbohydrate, nucleotide and/or lipid mediators; cellular activation state changes as determined by altered functional or structural properties of cells of the immune system, for example cell proliferation, altered motility, induction of specialized activities such as specific gene expression or cytolytic behavior; cellular differentiation by cells of the immune system, including altered surface antigen expression profiles or the onset of apoptosis (programmed cell death); or any other criterion by which the presence of an immune response may be detected.

Immune responses may often be regarded, for instance, as discrimination between self and non-self structures by the cells and tissues of a host's immune system at the molecular and cellular levels, but the invention should not be so limited. For example, immune responses may also include immune system state changes that result from immune recognition of self molecules, cells or tissues, as may accompany any number of normal conditions such as typical regulation of immune system components, or as may be present in pathological conditions such as the inappropriate autoimmune responses observed in autoimmune and degenerative diseases. As another example, in addition to induction by up-regulation of particular immune system activities (such as antibody and/or cytokine production, or activation of cell mediated immunity) immune responses may also include suppression, attenuation or any other down-regulation of detectable immunity, which may be the consequence of the antigen selected, the route of antigen administration, specific tolerance induction or other factors.

Certain embodiments of the present invention relate to modulating an immune function in a subject by administering an agent that alters SPL activity, for treating or preventing allergy. Allergic immune response mechanisms are well known in the art and include an antigen (e.g., allergen)-specific component such as an immunoglobulin (e.g., IgE), as well as the cells and mediators which comprise sequelae to allergen-immunoglobulin (e.g., IgE) encounters (e.g., Ott et al., 2000 J. Allerg. Clin. Immunol. 106:429; Barnes, 2000J. Allerg. Clin. Immunol. 106:5; Togias, 2000 J. Allerg. Clin. Immunol. 105:S599; Akdis et al., 2000 Int. Arch. Allerg. Immunol. 121:261; Beach, 2000 Occup. Med. 15:455).

According to certain other embodiments provided herein, immune function may be modulated in a subject by administering an agent that alters SPL activity, for treating or preventing transplantation graft rejection. Such grafts may, by way of non-limiting examples, be solid organ grafts or may alternatively be hematopoietic grafts, and graft rejection may be determined according to accepted criteria in the relevant medical arts, including classic host rejection of, e.g., allograft or xenograft tissue, and also including, e.g., graft-versus-host disease (GVHD) as may, for instance, accompany bone marrow transplantation following myeloablation in a therapeutic regimen for treating cancer.

In certain embodiments the present invention relates to a method of modulating immune function in a subject that comprises administering an agent that alters SPL activity, for purposes of treating or preventing an autoimmune disease, i.e., a disease, disorder or condition wherein a host immune system generates an inappropriate anti-“self” immune reaction. Such an autoimmune response may be characterized by the production of anti-“self” reactive antibodies (autoantibodies) and/or by induction of antigen-specific or non-specific cell-mediated and/or soluble mediator-driven autoimmune reactions, including inflammatory cascades. Examples of autoimmune diseases for which modulation of immune function may be beneficially applied according to certain invention embodiments include autoimmune diabetes (e.g., Type I diabetes mellitus), rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, Crohn's disease, and other autoimmune conditions.

Immune function modulating agents may be used to modulate, modify or otherwise alter (e.g., increase or decrease) cellular responses such as immune system cell proliferation, differentiation and survival, in a variety of contexts, both in vivo and in vitro. Thus, modulation of an immune function may in certain embodiments pertain to altering the proliferation or survival of one or a plurality of immune system cells. A wide variety of methodologies for determining cellular proliferation is known in the art and may have application to certain embodiments disclosed herein for purposes of identifying altered (e.g., increased or decreased with statistical significance) immune system cell proliferation in a subject or in a biological sample from a subject. Such techniques include, but are not limited to, cytological, biochemical, histochemical, radiochemical or immunochemical staining of cells for characteristic proliferation-associated (e.g., metaphase chromosome stains, DNA stains such as propidium iodide, ³H-thymidine incorporation, MTT staining) or cell cycle markers (e.g., Rabinovitch, 1994 Meths. Cell Biol. 41:263-296) or the like.

Cells that are suspected of undergoing apoptosis may be examined for morphological, permeability or other changes that are indicative of an apoptotic state. For example by way of illustration and not limitation, apoptosis in many cell types may cause altered morphological appearance such as plasma membrane blebbing, cell shape change, loss of substrate adhesion properties or other morphological changes that can be readily detected by a person having ordinary skill in the art, for example by using light microscopy. As another example, cells undergoing apoptosis may exhibit fragmentation and disintegration of chromosomes, which may be apparent by microscopy and/or through the use of DNA-specific or chromatin-specific dyes that are known in the art, including fluorescent dyes. Such cells may also exhibit altered plasma membrane permeability properties as may be readily detected through the use of vital dyes (e.g., propidium iodide, trypan blue) or by the detection of lactate dehydrogenase leakage into the extracellular milieu. Another readily practiced method for detecting apoptotic cells relates to detection of altered plasma membrane outer leaflet phospholipid composition in such cells, as determined, for instance, by quantification of phosphatidylserine exteriorization in the plasma membrane using detectably labeled annexin V (e.g., Fadok et al., J. Immunol. 148:2207, 1992). These and other means for detecting apoptotic cells by morphologic criteria, altered plasma membrane permeability and related changes will be apparent to those familiar with the art.

Apopotosis may also be determined by an assay for induction of specific protease activity in any member of a family of apoptosis-activated proteases known as the caspases (see, e.g., Green et al., 1998 Science 281:1309). Those having ordinary skill in the art will be readily familiar with methods for determining caspase activity, for example by determination of caspase-mediated cleavage of specifically recognized protein substrates. These substrates may include, for example, poly-(ADP-ribose) polymerase (PARP) or other naturally occurring or synthetic peptides and proteins cleaved by caspases that are known in the art (see, e.g., Ellerby et al., 1997 J. Neurosci. 17:6165). The synthetic peptide Z-Tyr-Val-Ala-Asp-AFC (SEQ ID NO:10), wherein “Z” indicates a benzoyl carbonyl moiety and AFC indicates 7-amino-4-trifluoromethylcoumarin (Kluck et al., 1997 Science 275:1132; Nicholson et al., 1995 Nature 376:37), is one such substrate. Other non-limiting examples of substrates include nuclear proteins such as U1-70 kDa and DNA-PKcs (Rosen and Casciola-Rosen, 1997 J. Cell. Biochem. 64:50; Cohen, 1997 Biochem. J. 326:1). Cellular apoptosis may also be detected by determination of cytochrome c that has escaped from mitochondria in apoptotic cells (e.g., Liu et al., Cell 86:147, 1996). Such detection of cytochrome c may be performed spectrophotometrically, immunochemically or by other well established methods for determining the presence of a specific protein. Alternatively, apoptosis or necrosis of the cell, and/or modulation of the functioning of the cell cycle within the cell, may be detected using art-established criteria. (See, e.g., Ashkenazi et al., 1998 Science, 281:1305; Thornberry et al., 1998 Science 281:1312; Evan et al., 1998 Science 281:1317; Adams et al., 1998 Science 281:1322; and references cited therein; see also, e.g., Wyllie, 1980 Nature 284:555; Arends et al., 1990 Am. J. Pathol. 136:593.) Persons having ordinary skill in the art will readily appreciate that there may be other suitable techniques for quantifying apoptosis.

Agents that alter SPL activity are described herein and additional suitable agents for use according to the present embodiments may be identified according to routine methodologies, such as those described in the herein incorporated references. For instance, methods of detecting SPL activity, and of screening compound libraries for agents that alter SPL activity, including polynucleotide sequences for the production of nucleic acid molecules that encode SPL polypeptides and the production of SPL polypeptides therefrom, are disclosed in U.S. application Ser. No. 10/348,052, U.S. application Ser. No. 10/622,011, and PCT/US2003/01739, including in publications cited therein (e.g., Van Veldhoven and Mannaerts, 1991 J. Biol. Chem. 266:12502-07) and elsewhere. For embodiments that relate to molecular biology methodologies, compositions and methods well known to those of ordinary skill in the art are described for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 1989; Ausubel et al. (1993 Current Protocols in Molecular Biology, Greene PubI. Assoc. Inc. & John Wiley & Sons, Inc., Boston, Mass.); Maniatis et al. (1982 Molecular Cloning, Cold Spring Harbor Laboratory, Plainview, N.Y.) and elsewhere. Certain embodiments as provided herein expressly contemplate a method of modulating immune function in a subject that comprises administering an agent that alters SPL activity wherein the agent is not FTY720 or myriocin, but certain other embodiments are not so limited and may include embodiments wherein a method of modulating immune function comprises administering FTY720 and/or myriocin, optionally in combination with one or more additional agents, such as an agent that alters SPL activity and/or an agent that alters SK activity and/or an agent that alters a level of S1P or an interaction between S1P and an S1P receptor such as S1P₁ (or another G protein-coupled S1P receptor), or another agent.

In certain other embodiments a method of modulating immune function in a subject is expressly contemplated that comprises administering an agent that alters SPL activity wherein the agent is at least one of deoxypyridoxine, C₈₋cyclopropenylceramide and C₁₆-cyclopropenylceramide, each of which has been shown to be capable of altering SPL activity (see, e.g., Triola et al., 2004 Mol. Pharmacol. 66:1671; see also Matreya LLC 2005 Catalog (Pleasant Gap, Pa.), Cat. Nos. 1886 and 1887).

As also provided herein, certain contemplated embodiments relate to a method of modulating immune function in a subject by administering an agent that decreases SPL activity, which in certain embodiments may involve an agent that decreases SPL activity by directly binding to SPL, while in certain other embodiments an agent that decreases SPL activity may do so indirectly, for example, by interacting with other cellular molecular components that exert an effect on SPL activity. Certain contemplated embodiments relate to an agent that is capable of decreasing SPL activity by causing a decreased expression level of SPL.

Compositions and methods directed to altering (e.g., increasing or decreasing with statistical significance) SPL expression levels are described in U.S. Pat. No. 6,423,527; U.S. Pat. No. 6,569,666; U.S. Pat. No. 6,495,359; U.S. application Ser. No. 10/053,510; U.S. application Ser. No. 10/286,175; U.S. application Ser. No. 10/197,073; U.S. application Ser. No. 10/348,052; U.S. application Ser. No. 10/622,011; and PCT/US2003/01739, wherein can be found abundant disclosure describing nucleic acid molecules that encode SPL polypeptides, including SPL-encoding polynucleotides (and nucleotides that hybridize thereto under moderately stringent conditions, which may be, e.g., prewashing in a solution of 5×SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50-65° C., 5×SSC, overnight; followed by washing twice at 65° C. for 20 minutes with each of 2×, 0.5× and 0.2×SSC containing 0.1% SDS) and encoded SPL polypeptide sequences, and wherein also can be found description of antibodies that specifically bind to a translated polypeptide product of an SPL-encoding nucleic acid molecule. Certain embodiments contemplated herein thus include the use of all or a portion of such an SPL-encoding polynucleotide and/or a polynucleotide that hybridizes thereto under moderately stringent conditions, for example, a polynucleotide that comprises all or a portion of the nucleotide sequence set forth in any one of SEQ ID NOS:1, 3, 5, 7 and 9.

According to certain related embodiments, an agent that causes a decreased SPL expression level may be an antisense polynucleotide that specifically hybridizes to a nucleic acid molecule that encodes a SPL polypeptide, a ribozyme that specifically cleaves a nucleic acid molecule that encodes a SPL polypeptide, a small interfering RNA that is capable of interfering with a nucleic acid molecule that encodes a SPL polypeptide, or an agent that alters activity of a regulatory element that is operably linked to a nucleic acid molecule that encodes a SPL polypeptide. As disclosed herein and known to the art, such nucleic acid sequence-based agents can be readily prepared using routine methodologies

A polynucleotide that is complementary to at least a portion of a coding sequence (e.g., an antisense polynucleotide or a ribozyme) may thus be used to modulate SPL-encoding gene expression. Identification of oligonucleotides and ribozymes for use as antisense agents, and DNA encoding genes for their targeted delivery, involve methods well known in the art. For example, the desirable properties, lengths and other characteristics of such oligonucleotides are well known. Antisense oligonucleotides are typically designed to resist degradation by endogenous nucleolytic enzymes by using such linkages as: phosphorothioate, methylphosphonate, sulfone, sulfate, ketyl, phosphorodithioate, phosphoramidate, phosphate esters, and other such linkages (see, e.g., Agrwal et al., Tetrahedron Lett. 28:3539-3542 (1987); Miller et al., J. Am. Chem. Soc. 93:6657-6665 (1971); Stec et al., Tetrahedron Lett. 26:2191-2194 (1985); Moody et al., Nucl. Acids Res. 12:4769-4782 (1989); Uznanski et al., Nucl. Acids Res. (1989); Letsinger et al., Tetrahedron 40:137-143 (1984); Eckstein, Annu. Rev. Biochem. 54:367-402 (1985); Eckstein, Trends Biol. Sci. 14:97-100 (1989); Stein In: Oligodeoxynucleotides. Antisense Inhibitors of Gene Expression, Cohen, Ed, Macmillan Press, London, pp. 97-117 (1989); Jager et al., Biochemistry 27:7237-7246 (1988)).

Antisense polynucleotides are oligonucleotides that bind in a sequence-specific manner to nucleic acids, such as mRNA or DNA. When bound to mRNA that has complementary sequences, antisense prevents translation of the mRNA (see, e.g., U.S. Pat. No. 5,168,053 to Altman et al.; U.S. Pat. No. 5,190,931 to Inouye, U.S. Pat. No. 5,135,917 to Burch; U.S. Pat. No. 5,087,617 to Smith and Clusel et al. (1993) Nucl. Acids Res. 21:3405-3411, which describes dumbbell antisense oligonucleotides). Triplex molecules refer to single DNA strands that bind duplex DNA forming a colinear triplex molecule, thereby preventing transcription (see, e.g., U.S. Pat. No. 5,176,996 to Hogan et al., which describes methods for making synthetic oligonucleotides that bind to target sites on duplex DNA).

Particularly useful antisense nucleotides and triplex molecules are molecules that are complementary to or bind the sense strand of DNA or mRNA that encodes a SPL polypeptide or a protein mediating any other process related to expression of endogenous SPL, such that inhibition of translation of mRNA encoding the SPL polypeptide is effected. cDNA constructs that can be transcribed into antisense RNA may also be introduced into cells or tissues to facilitate the production of antisense RNA. Antisense technology can be used to control gene expression through interference with binding of polymerases, transcription factors or other regulatory molecules (see Gee et al., In Huber and Carr, Molecular and Immunologic Approaches, Futura Publishing Co. (Mt. Kisco, N.Y.; 1994)). Alternatively, an antisense molecule may be designed to hybridize with a control region of a SPL-encoding gene (e.g., promoter, enhancer or transcription initiation site), and block transcription of the gene; or to block translation by inhibiting binding of a transcript to ribosomes.

The present invention also contemplates use of SPL-encoding nucleic acid sequence-specific ribozymes. A ribozyme is an RNA molecule that specifically cleaves RNA substrates, such as mRNA, resulting in specific inhibition or interference with cellular gene expression. There are at least five known classes of ribozymes involved in the cleavage and/or ligation of RNA chains. Ribozymes can be specifically targeted to any RNA transcript and can catalytically cleave such transcripts (see, e.g., U.S. Pat. No. 5,272,262; U.S. Pat. No. 5,144,019; and U.S. Pat. Nos. 5,168,053, 5,180,818, 5,116,742 and 5,093,246 to Cech et al.). Any SPL mRNA-specific ribozyme, or a nucleic acid encoding such a ribozyme, may be delivered to a host cell to effect inhibition of SPL gene expression. Ribozymes may therefore be delivered to the host cells by DNA encoding the ribozyme linked to a eukaryotic promoter, such as a eukaryotic viral promoter, such that upon introduction into the nucleus, the ribozyme will be directly transcribed. Particularly useful sequence regions of a SPL-encoding mRNA for use as a ribozyme target can be found using routine sequence alignment tools known to the art such as BLAST or MegAlign, and may preferably be sequence stretches that are unique to the SPL-encoding mRNA relative to other transcribed sequences that may be present in a particular cell. In one preferred example, a ribozyme may be designed and constructed such that it is targeted to bind to a region of SPL-encoding mRNA that encodes a portion of the human SPL polypeptide containing the lysine residue found at amino acid position 353 therein, but the invention is not so limited and other ribozymes targeted to other regions of SPL-encoding mRNA are also contemplated.

Any polynucleotide may be further modified to increase stability in vivo. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends; the use of phosphorothioate or 2′ O-methyl rather than phosphodiester linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl-methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.

RNA interference (RNAi) is a polynucleotide sequence-specific, post-transcriptional gene silencing mechanism effected by double-stranded RNA that results in degradation of a specific messenger RNA (mRNA), thereby reducing the expression of a desired target polypeptide encoded by the mRNA (see, e.g., WO 99/32619; WO 01/75164; U.S. Pat. No. 6,506,559; Fire et al., Nature 391:806-11 (1998); Sharp, Genes Dev. 13:139-41 (1999); Elbashir et al. Nature 411:494-98 (2001); Harborth et al., J. Cell Sci. 114:4557-65 (2001)). “Small interfering RNA” (siRNA) or DNP-RNA polynucleotides that interfere with expression of specific polypeptides in higher eukaryotes such as mammals (including humans) have been considered (e.g., Karagiannis and El-Osta, 2005 Cancer Gene Ther. May 2005, PMID: 15891770; Chen et al., 2005 Drug Discov. Today 10:587; Scherr et al., 2005 Curr. Opin. Drug Discov. Devel. 8:262; Tomari and Zamore, 2005 Genes Dev. 19:517; see also, e.g., Tuschl, 2001 Chembiochem. 2:239-245; Sharp, 2001 Genes Dev. 15:485; Bernstein et al., 2001 RNA 7:1509; Zamore, 2002 Science 296:1265; Plasterk, 2002 Science 296:1263; Zamore 2001 Nat. Struct. Biol. 8:746; Matzke et al., 2001 Science 293:1080; Scadden et al., 2001 EMBO Rep. 2:1107; Hutvagner et al., Curr. Opin. Gen. Dev. 12:225-32 (2002); Elbashir et al., 2001; Nykänen et al., Cell 107:309-21 (2001); Bass, Cell 101:235-38 (2000)); Zamore et al., Cell 101:25-33 (2000)). Transfection of human and other mammalian cells with double-stranded RNAs of about 18-27 nucleotide base pairs in length interferes in a sequence-specific manner with expression of particular polypeptides encoded by messenger RNAs (mRNA) containing corresponding nucleotide sequences (WO 01/75164; Elbashir et al., 2001; Elbashir et al., Genes Dev. 15:188-200 (2001)); Harborth et al., J. Cell Sci. 114:4557-65 (2001); Carthew et al., Curr. Opin. Cell Biol. 13:244-48 (2001); Mailand et al., Nature Cell Biol. Advance Online Publication (Mar. 18, 2002); Mailand et al. 2002 Nature Cell Biol. 4:317). SPL-specific siRNA constructs are available and have been obtained from Dharmacon (Lafayette, Colo.). In certain non-limiting embodiments double-stranded RNAs for use in RNAi may have, for example, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32 or more nucleotide base pairs.

As noted above, in certain embodiments the agent that causes a decreased SPL expression level may alter activity of a regulatory element that is operably linked to a nucleic acid molecule that encodes a SPL polypeptide. According to a related embodiment the regulatory element comprises a GATA transcription factor-binding motif (Oskouian et al., 2005 J. Biol. Chem. 280:18403-410). By way of representative example and not limitation, these and related embodiments contemplate suitable agents that are capable of down-regulating SPL activity by suppressing or repressing transcription of SPL-encoding genes, which agents can be readily identified using art-accepted methodologies to screen for functional blockers of SPL gene transcription. For instance, Oskouian et al. (2005) describe regulation of the human SPL gene by a GATA transcription factor that interacts with an upstream regulatory element, as characterized using a reporter gene transcriptional run-off assay that can be readily adapted to screen for functional inhibitors of SPL gene expression. Using such an approach, agents capable of causing decreased SPL expression levels may be identified from compound libraries such as libraries of synthetic (e.g., combinatorial chemistry) small molecules, or natural products libraries, or recombinant expression libraries, or other sources.

Certain other embodiments as disclosed herein contemplate a method of modulating immune function in a subject that comprises administering an agent that alters sphingosine-1-phosphate lyase (SPL) activity, wherein the agent is selected from (a) a mutated form of a nucleic acid molecule that encodes a SPL polypeptide wherein the mutated form encodes a dominant negative mutant SPL polypeptide, or a complementary polynucleotide thereto, and (b) a dominant negative mutant SPL polypeptide encoded by (a). The nucleic acid molecule that encodes a SPL polypeptide is described above and in several above-referenced patents and patent applications, e.g., U.S. application Ser. No. 10/348,052, U.S. application Ser. No. 10/622,011, and PCT/US2003/01739, including in publications cited therein (e.g., Van Veldhoven and Mannaerts, 1991 J. Biol. Chem. 266:12502-07), as are compositions and methods for introducing mutations (see, e.g., Sambrook et al., 1989; Ausubel et al., 1993; Maniatis et al., 1982). Principles and practices directed to functional inactivation of a desired target gene using a dominant negative mutation are described in Herskowitz et al. (1987 Nature 329:219-222) and in Perlmutter et al. (1996 Curr. Opin. Immunol. 8:285-290). Without wishing to be bound by theory, according to these and related embodiments a dominant negative mutant SPL may be engineered and functionally identified using routine methodologies as described herein and in the cited references, such that introduction of the dominant negative mutant (e.g., by administering a mutated SPL-encoding nucleic acid molecule by suitable art-accepted methodologies such as transfection, electroporation, biolistics, naked DNA, plasmid, viral vector, liposomal delivery or other suitable means, or by administering a mutant SPL polypeptide) in a manner and for a time sufficient to obtain an immune system cell having the dominant negative SPL, results in competition for substrate (e.g., S1P) between wildtype (endogenous) SPL and the dominant negative mutant SPL, thereby effectively decreasing the effective level of SPL activity in the cell.

Therapeutic Methods

One or more agents that alter SPL activity as provided herein and/or as identified according to the above-described methods may also be used to modulate immune function in a subject. As used herein, a “subject” may be any mammal, including a human, and may be afflicted with a condition associated with inappropriate or undesired immunological activity or may be free of any detectable disease, disorder or condition of abnormal immune function. Accordingly, the treatment may be of an existing disease or may be prophylactic. Conditions for which it may be desirable to modulate immune function include any disorder associated with cell proliferation, including inflammation, transplant graft rejection (e.g., allograft rejection or graft-versus-host disease (GVHD)), autoimmune diseases, allergy or other conditions.

For administration to a patient, one or more agents that alter SPL activity are generally formulated as a pharmaceutical composition. A pharmaceutical composition may be a sterile aqueous or non-aqueous solution, suspension or emulsion, which additionally comprises a physiologically acceptable carrier (i.e., a non-toxic material that does not interfere with the activity of the active ingredient). Such compositions may be in the form of a solid, liquid or gas (aerosol). Alternatively, compositions of the present invention may be formulated as a lyophilizate or compounds may be encapsulated within liposomes using well known technology. Pharmaceutical compositions within the scope of the present invention may also contain other components, which may be biologically active or inactive. Such components include, but are not limited to, buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, chelating agents such as EDTA or glutathione, stabilizers, dyes, flavoring agents, and suspending agents and/or preservatives.

Any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of the present invention. Carriers for therapeutic use are well known, and are described, for example, in Remingtons Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro ed. 1985). In general, the type of carrier is selected based on the mode of administration. Pharmaceutical compositions may be formulated for any appropriate manner of administration, including, for example, topical, oral, nasal, intrathecal, rectal, vaginal, sublingual or parenteral administration, including subcutaneous, intravenous, intramuscular, intrasternal, intracavernous, intrameatal or intraurethral injection or infusion. For parenteral administration, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, kaolin, glycerin, starch dextrins, sodium alginate, carboxymethylcellulose, ethyl cellulose, glucose, sucrose and/or magnesium carbonate, may be employed.

A pharmaceutical composition (e.g., for oral administration or delivery by injection) may be in the form of a liquid (e.g., an elixir, syrup, solution, emulsion or suspension). A liquid pharmaceutical composition may include, for example, one or more of the following: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer's solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium, polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. A parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. The use of physiological saline is preferred, and an injectable pharmaceutical composition is preferably sterile.

The compositions described herein may be formulated for sustained release (i.e., a formulation such as a capsule or sponge that effects a slow release of compound following administration). Such compositions may generally be prepared using well known technology and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site. Sustained-release formulations may contain an agent dispersed in a carrier matrix and/or contained within a reservoir surrounded by a rate controlling membrane. Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature of the condition to be treated or prevented.

Within a pharmaceutical composition, a therapeutic agent comprising one or more agents that alter SPL activity may be linked to any of a variety of compounds. For example, such an agent may be linked to a targeting moiety (e.g., a monoclonal or polygonal antibody, a protein or a liposome) that facilitates the delivery of the agent to the target site. As used herein, a “targeting moiety” may be any substance (such as a compound or cell) that, when linked to an agent enhances the transport of the agent to a target cell or tissue, thereby increasing the local concentration of the agent. Targeting moieties include antibodies or fragments thereof, receptors, ligands and other molecules that bind to cells of, or in the vicinity of, the target tissue. An antibody targeting agent may be an intact (whole) molecule, a fragment thereof, or a functional equivalent thereof. Examples of antibody fragments are F(ab′)₂, Fab′, Fab and F[v] fragments, which may be produced by conventional methods or by genetic or protein engineering. Linkage is generally covalent and may be achieved by, for example, direct condensation or other reactions, or by way of bi- or multi-functional linkers. Targeting moieties may be selected based on the cell(s) or tissue(s) toward which the agent is expected to exert a therapeutic benefit.

Pharmaceutical compositions may be administered in a manner appropriate to the disease or condition to be treated (or prevented). An appropriate dosage and a suitable duration and frequency of administration will be determined by such factors as the condition of the patient, the type and severity of the patient's disease, the particular form of the active ingredient and the method of administration. In general, an appropriate dosage and treatment regimen provides the agent(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit (e.g., an improved clinical outcome, such as more frequent complete or partial remissions, or longer disease-free and/or overall survival, or a lessening of symptom severity). For prophylactic use, a dose should be sufficient to prevent, delay the onset of or diminish the severity of a disease associated with cell proliferation.

Optimal dosages may generally be determined using experimental models and/or clinical trials. In general, the amount of an agent that alters SPL activity present in a dose, ranges from about 0.01 μg to about 100 μg per kg of host, typically from about 0.1 μg to about 10 μg. The use of the minimum dosage that is sufficient to provide effective therapy is usually preferred. Patients may generally be monitored for therapeutic or prophylactic effectiveness using assays suitable for the condition being treated or prevented, which will be familiar to those having ordinary skill in the art. Suitable dose sizes will vary with the size of the patient, but will typically range from about 10 mL to about 500 mL for 10-60 kg animal.

The following Examples are offered by way of illustration and not limitation.

EXAMPLES Example 1 Experimental Procedures

Materials: FTY720 and FTY720-P were provided by Volker Brinkmann of Novartis (Basel, Switzerland). C17 and C18 sphingosines, PSo and S1Ps were obtained from Biomol Research Laboratories, Inc. (Plymouth Meeting, Pa.). [4,5³H]-D-erythro-DHS 1-P was obtained from American Radiolabeled Chemicals, Inc. (St. Louis, Mo.). All other chemicals including 1-butanol and o-phthalaldehyde (OPA) were purchased from Sigma/Aldrich (St. Louis, Mo.). GT11 (C8 and C16 analogues) was obtained from Matreya LLC (Pleasant Gap, Pa.).

FTY720-P metabolism: Whole cell extracts of HEK293 cells stably overexpressing human SPL were prepared as previously described (Reiss et al., (2004) J Biol Chem 279, 1281-1290). These extracts contained approximately 700 picomoles/mg protein/minute of SPL activity. Twenty nanomoles FTY720-P were suspended in SPL reaction buffer (Van Veldhoven et al., (1991) J Biol Chem 266, 12502-12507), and 25 microliters of whole cell extract were added to initiate the reaction. At various time points, reaction was stopped by addition of a 2 ml mixture of chloroform and methanol (2:1 v/v), 1 ml of 1M KCl, 0.1 ml concentrated HCl. Sample was mixed by vortexing and centrifuged at 1200 rpm for 5 min. Organic phase was collected, dried down using a speed vac and resuspended in methanol. After derivatization with OPA, the sample was injected onto the HPLC for quantification. The HPLC analysis was conducted using a Beckman (Torrance, Calif., USA) system Gold 125 solvent module with a Spectra-Physics SP8410 fluorescence detector and a C18 (2) Luna 3 μm, 75×4.6 mm column from Phenomenex (CA). The mobile phase was methanol:10 mM phosphate buffer pH 7.2:1 M tetrabutylammonium dihydrogen phosphate (TBAP) in water=83:16:1, v/v/v and the flow rate was 1 ml/min. The calculation of the FTY720-P in each sample was based on the integration of the peaks of interest and the comparison of the OPA derivative of untreated FTY720-P. For comparison, 10 nanomoles S1P were incubated with extracts from HEK293 cells overexpressing SPL or HEK293 cells containing vector, and extraction of S1P was performed as for FTY720. Recovery of S1P was determined by HPLC quantitation, as described below for S1P measurements in mouse tissues.

Confirmation of FTY720-P by LCMS: Samples corresponding to FTY720-P peak identified on HPLC were evaluated by LCMS to confirm FTY720-P by mass analysis. Twenty microliters of sample were injected into the LCMS and mass spectrum scans from 300 to 500 m/z and specific ions m/Z 388 and 410 were quantified for FTY720-P. A reverse phase C18 column from Phenomenex (2.1 mm×15 cm) was used. Two mobile phases were used: solution A is water:methanol:acetic acid (69:30:1) containing 5 mM ammonium acetate and solution B is methanol:acetic acid (99:1) containing 5 mM ammonium acetate. The program for these two mobile phases was started with 50% A and B, continued for 2 min and then B was increased to 100% in 6 min, continued for 5 min in 100% B and finally decreased B back to 50% in 2 min. The flow rate was 0.3 ml/min. The retention time was 11.2 min.

Drug treatments and leukocyte/lymphocyte counts: Four-week old FVB or C3H mice were obtained from Charles River Laboratories (Wilmington, Mass.). Animals were maintained in a pathogen-free facility in microisolator cages. Mice were anaesthetized with isoflurane inhalation, and a single dose of FTY720 (at 1 or 3 mg/kg) or GT11 (at 1, 10 or 100 mg/kg) in sterile water was injected intraperitoneally at time zero. Blood counts were determined by Coulter counter (Coulter Instruments, Hialeah, Fla.) and by manual differential counting. Mice were euthanized by CO₂ inhalation at various time points post-injection, followed by tissue harvest. All animal studies were performed in accordance with approved CHORI IACUC protocols.

SPL enzyme assay: Tissues were homogenized by sonication in 9 volumes of ice-cold homogenization buffer (5 mM MOPS pH 7.5, 1 mM DTT, 1 mM EDTA, 0.25 M sucrose, and 5 micrograms/ml each chymostatin, leupeptin, pepstatin A and antipain). SPL assays were conducted using 50 micrograms protein per assay and radioactive [4,5 ³H]DHS1P substrate, as described previously (Reiss et al., (2004) J Biol Chem 279, 1281-1290). For in vitro FTY720 and FTY720-P experiments, drug was incubated with whole cell extracts prepared from HEK293 cells infected with an adenoviral vector expressing human SPL. These extracts contained approximately 200 picomoles/mg protein/minute SPL activity. Drug was incubated with extracts for 30 minutes, followed by addition of extracts to reaction buffer and substrate to initiate the reaction.

S1P measurements: S1P was isolated by two-phase lipid extraction, derivatized with OPA and quantitated by HPLC essentially as described (Jiang et al, (2004) Proc Natl Acad Sci USA 101, 17825-17830; Fyrst et al., (2004) J Lipid Res 45, 54-62; Caligan et al., (2000) Anal. Biochem. 281, 36-44). All tissues were weighed prior to snap freezing in liquid nitrogen and were stored at −100° C. until processing. One nanomole of C¹⁷-S1P and PSo were added as internal standards before homogenization of tissues. Lipids were extracted with 1 ml mixture of chloroform and methanol (1:2 ratio). Samples were incubated at room temperature with sonication for 3 hours and then dried by speed vac. One ml of 0.1N NaOH in methanol was added for 1 hour at 37° C. to achieve hydrolysis. After addition of 4 ml chloroform and 4 ml 1M KCl, samples were mixed and phases separated by centrifugation. The organic phase was collected and dried for sphingosine determination. The aqueous phase was mixed with 300 μl concentrated HCl and 6 ml chloroform. The phases were separated by centrifugation, and the organic phase was collected and dried for S1P determination. All samples for S1P determination were re-dissolved in methanol. After derivation with OPA, samples were injected onto HPLC for quantification. The mobile phase was methanol: 10 mM phosphate buffer (pH 7.2): 1M tetrabutylammonium dihydrogen phosphate (TBAP) in water=83:16:1, v/v/v and the flow rate was 1 ml/min.

SPL expression: To evaluate the effect of FTY720 and FTY720-P on SPL gene expression, HEK293 cells were treated for 30 minutes with 3 μM of either drug, followed by transfection with pSPL-BamHI, a human SPL-luciferase reporter construct. After 48 hours, reporter expression was determined by luciferase activity as described (Oskouian et al., (2005) J Biol Chem 280, 18403-18410)). Western blotting of mouse tissue extracts was performed using a 1:2000 dilution of polyclonal sera raised against the murine SPL C-terminal peptide: (NH₂)-V-T-Q-G-N-Q-M-N-G-S—P-K-P—R—(COOH). [SEQ ID NO:11]

Cellular Immune Functions—Mitogen Induced Lymphoproliferation: Spleen and thymus tissues were harvested from wild type C3H mice, and cell suspensions were prepared as described previously (Mishell et al., (1980) in Selected Methods in Cellular Immunology (Mishell, B., and Shiigi, S., eds), pp. 3-27, WH Freeman and Company, San Francisco). Cells were dispersed in sterile medium in 96 well microtiter plates (Falcon) at a concentration of 1×10⁶ cells/ml for spleen and 5×10⁶ cells/ml for thymus. Cells were incubated in the presence or absence of GT11 for 24 hours at 37 C in 5% CO2, followed by treatment with 1 or 10 μg/ml LPS or vehicle control (BSS). Cell proliferation was determined after 48 and 72 hours using the Cell Titer 96 Non-Radioactive Cell Proliferation Assay from Promega (Mannheim, Germany), according to the manufacturer's instructions.

Example 2 FTY720 but not FTY720P Inhibits SPL Activity

SPL does not catabolize FTY720-P—FTY720 demonstrated a long elimination half-life after single dose administration (Brinkmann, (2004) Yonsei Med J 45, 991-997). Known routes of drug metabolism included conversion to FTY720-P by SK, and omega oxidation of the octyl side chain, followed by beta oxidation.

This Example describes testing of whether FTY720 might function as a substrate for SPL, which recognizes phosphorylated long chain bases of varying chain length, hydroxylation and saturation. First, FTY720-P was incubated under standard SPL assay conditions with HEK293 cells previously determined to demonstrate high levels of SPL activity by virtue of their stable expression of a human SPL-GFP fusion protein. Incubation proceeded for various lengths of time, after which FTY720-P was recovered by two-phase lipid extraction, derivatized with the fluorescent compound OPA and quantitated by HPLC. As shown in FIG. 1A, FTY720-P remained stable for up to 24 hours in the presence of SPL. In contrast, SIP levels diminished under the same conditions (FIG. 1B).

S1P levels following FTY720-P exposure in HEK293 cells that overexpressed SPL (Reiss et al., 2004 J Biol Chem 279:1281) were also compared to control green fluorescent protein (GFP)-transfectants, and S1P levels diminished in the SPL overexpressors but not in the GFP-expersing control cells. These results indicated that FTY720-P did not serve as a substrate for SPL under standard conditions.

Inhibition of SPL by FTY720 in vivo—The effect on SPL enzyme activity of FTY720 administration was tested. Four-week old female FVB mice were given 1 mg/kg FTY720 by intraperitoneal injection, and tissue SPL activity in thymus was assessed over time. As shown in FIG. 2, inhibition of SPL was noted as early as 12 hours after FTY720 treatment, peaked at 36 hours at approximately 40% inhibition, and began to reverse by 48 hours. SPL inhibition occurred concomitantly with lymphopenia, and was consistent with the timing of lymphopenia reported previously (Chiba et al., (1998) J Immunol 160, 5037-5044) (Table 1).

TABLE 1 Lymphocyte counts after FTY720 treatment Lymphocytes Time in Hours (1000/μL) SD 0 4.5 1.15 24 2.2 0.52 48 3.2 0.56 72 2.0 0.37

To address whether the inhibition of SPL activity in homogenates of tissues isolated from FTY720 treated animals was reversible, tissue SPL activity was measured in the presence of increasing amounts of non-radiolabeled DHS1P substrate. Enzyme inhibition (21%) that was observed in tissues from animals treated with FTY720 for 24 hours was partially overcome (reduced to 14% inhibition) by a 2-fold increase in unlabeled substrate, whereas the level of inhibition in the presence of 40 nmol unlabeled substrate (25%) was similar to that observed with 10 nmol of substrate (standard assay conditions).

In separate experiments, SPL expression in vivo was detected in the thymus and in intestinal inflammatory cells by immunohistochemistry. Briefly, polyclonal rabbit anti-murine SPL antisera (see, e.g., U.S. Pat. No. 7,041,291) were diluted 1:200 in 0.5% ovalbumin/PBS and incubated with murine thymic and intestinal tissue sections from normal 129svIC57BL/6 mice and, as a control, from SPL-deficient embryonic stem cell SPL^(−/−) (Sgpl^(−/−)) knockout mice generated in the 129sv/C57BL/6 background according to established methodologies (Chen et al., 2004 Nature Genetics 36:304). Sections were then rinsed and developed using biotinylated anti-rabbit immunoglobulin (Vector Laboratories, Burlingame, Calif.) and the EliteABC™ kit (Vector) according to the manufacturer's instructions. No staining was observed in tissues from the SPL^(−/−) (Sgpl^(−/−)) knockout mice, confirming the specificity of the antibodies in the rabbit anti-murine SPL antisera. In the normal (SPL^(+/+)) animals, however, SPL was localized immunohistochemically to thymic epithelium in thymus sections, and to inflammatory cells apparently including lymphocytes in intestinal tissue sections.

Inhibition of SPL activity by FTY720 in vitro—To determine whether the effect of FTY720 on SPL activity was due to a direct interaction between the SPL enzyme and the long chain base analog in either its phosphorylated or unphosphorylated form, whole cell extracts were prepared from HEK293 cells expressing high levels of SPL by virtue of an SPL-adenoviral construct and incubated with varying concentrations of FTY720 or FTY720-P. As shown in FIG. 3A, FTY720 inhibited SPL activity in vitro in a dose-dependent fashion, with effects occurring as low as 300 nM and maximal effect observed at 30 μM. In contrast, FTY720-P was inhibitory only at 30 μM, and the effect was not dose-dependent. Although treatment with FTY720 was associated with low (nanomolar) circulating drug levels, it was possible that local concentrations within cells and subcellular compartments may have been considerably higher, since FTY720 has been reported to be actively transported into cells by the actions of drug transporters that recognize long chain bases (Honig et al., (2003) J Clin Invest 111, 627-637).

Example 3 FTY720 Effects on SPL In Vivo

FTY720 effect on SPL gene or protein expression—SPL gene expression was inducible by GATA transcription factors (Oskouian et al., (2005) J Biol Chem 280, 18403-18410) and other physiological conditions, including DNA damage, hypoxia, and other stress conditions (unpublished observations). Therefore, SPL expression was examined in the tissues of mice treated with FTY720, as well as in cell lines exposed to FTY720. Neither SPL gene expression as determined by a SPL-luciferase reporter system (FIG. 4A) nor tissue SPL protein expression as determined by immunoblotting (FIG. 4B) appeared to be affected by FTY720 treatment at doses that inhibited enzyme activity. These studies confirmed that the major effect of the drug on SPL activity is through a post-translational mechanism.

FTY720 administration minimally affects tissue SIP levels-SK is known to be responsible for S1P synthesis, whereas SPL and S1P phosphatases are responsible for S1P catabolism. Since FTY720 interacts with both SK and SPL and may potentially influence the efficiency of both S1P synthesis and degradation, the sum effect of FTY270 administration on tissue S1P levels was determined. FTY720 treatment was associated with a slight increase in thymic tissue S1P at 36 hours, followed by a return to baseline levels by 48 hours (Table 2). Dihydrosphingosine-1-P levels also remained stable throughout 48 hours of treatment (data not shown). S1P levels increased somewhat more dramatically in splenic tissue after FTY720 treatment (Table 2). DHS1P levels remained stable throughout 48 hours of treatment. These findings indicated that, despite potential competition with sphingosine by FTY720 as a substrate for sphingosine kinases, tissue SIP levels did not decrease and may have increased transiently. According to non-limiting theory, simultaneous inhibition of SPL may account for the stability of tissue S1P levels in response to drug treatment.

TABLE 2 S1P levels in murine tissue after FTY720 treatment Time in S1P Hours (thymus)¹ S.D. 0 3375.50 1358.26 24 3000.69 1382.10 36 3917.48 184.67 48 3194.45 1162.69 Time in S1P S1P Hours (thymus)¹ S.D. (spleen)¹ S.D. 0 3152.00 1053.90 10229.65 357.02 24 3000.69 1382.10 15121.31 4009.99 36 3917.48 184.67 18482.30 302.34 48 3194.45 1162.69 12365.84 128.65 Values are picomoles per gram of wet weight tissue; n = 4 animals per time point (S.D., standard deviation)

In summary, these studies demonstrated that FTY720 inhibited the activity of SPL, the major enzyme responsible for irreversibly removing S1P from the sphingosine-S1P cycle. This effect was observed in vivo at therapeutic doses of the drug and concomitant with lymphopenia and in vitro at somewhat higher concentrations. Further according to non-limiting theory, inhibition of SPL by FTY720 may have limited FTY720 cytotoxicity by preventing S1P depletion during conversion of the drug to its phosphorylated form.

Mitogen Induced Lymphoproliferation—LPS-stimulated cellular proliferation under conditions described above in Example 1 was quantified using two different dosages of an SPL inhibitor, GT111 (C8 analogue) and the results are depicted in FIG. 5. Lymphoproliferation was reduced in the presence of the SPL inhibitor. Examination by light microscopy of samples of cells recovered from control and experimental cell cultures indicated that non-specific cytotoxic effects of GT11 were negligible.

ADDITIONAL PUBLICATIONS CITED

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All of the above U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheet, are incorporated herein by reference, in their entirety.

From the foregoing it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the invention. Accordingly, the invention is not limited except as by the appended claims. 

1. A method of modulating immune function in a subject, comprising administering to the subject an agent that alters sphingosine-1-phosphate lyase (SPL) activity, and thereby modulating immune function.
 2. The method of claim 1 wherein modulating immune function comprises reducing or preventing tissue inflammation in the subject.
 3. The method of claim 1 wherein modulating immune function comprises treating or preventing a condition that is selected from the group consisting of transplant graft rejection, autoimmune disease and allergy.
 4. The method of claim 1 wherein modulating immune function comprises altering proliferation or survival of an immune system cell.
 5. The method of claim 4 wherein the immune system cell is a lymphocyte or a hematopoietic cell of lymphoid lineage.
 6. The method of claim 1 wherein the agent that alters sphingosine-1-phosphate lyase (SPL) activity is capable of decreasing SPL activity.
 7. The method of claim 6 wherein the agent that is capable of decreasing SPL activity binds to SPL.
 8. The method of claim 6 wherein the agent that is capable of decreasing SPL activity causes a decreased expression level of SPL.
 9. The method of claim 8 wherein the agent that causes a decreased expression level of SPL is selected from the group consisting of: (a) an antisense polynucleotide that specifically hybridizes to a nucleic acid molecule that encodes a SPL polypeptide, (b) a ribozyme that specifically cleaves a nucleic acid molecule that encodes a SPL polypeptide, (c) a small interfering RNA that is capable of interfering with a nucleic acid molecule that encodes a SPL polypeptide, (d) an agent that alters activity of a regulatory element that is operably linked to a nucleic acid molecule that encodes a SPL polypeptide, and (e) an antibody that specifically binds to a translated product of a nucleic acid molecule that encodes a SPL polypeptide, wherein the nucleic acid molecule that encodes a SPL polypeptide is selected from the group consisting of (i) a nucleic acid molecule comprising a nucleotide sequence as set forth in SEQ ID NO:1 or a complementary sequence thereto, or as set forth in SEQ ID NO:3 or a complementary sequence thereto, (ii) a nucleic acid molecule comprising a nucleotide sequence that hybridizes under moderately stringent conditions to the nucleic acid molecule of (i) and that encodes a polypeptide having sphingosine-1-phosphate lyase (SPL) activity, and (iii) a nucleic acid molecule that encodes a SPL polypeptide which comprises an amino acid sequence as set forth in SEQ ID NO:2 or a portion of SEQ ID NO:2 having sphingosine-1-phosphate lyase (SPL) activity, or as set forth in SEQ ID NO:4 or a portion of SEQ ID NO:4 having sphingosine-1-phosphate lyase (SPL) activity.
 10. The method of claim 1 wherein the agent that alters sphingosine-1-phosphate lyase (SPL) activity is not FTY720 or myriocin.
 11. The method of claim 1 wherein the agent that alters sphingosine-1-phosphate lyase (SPL) activity is selected from the group consisting of deoxypyridoxine, C₈-cyclopropenylceramide and C₁₆-cyclopropenylceramide.
 12. The method of claim 1 wherein the agent that alters sphingosine-1-phosphate lyase (SPL) activity alters activity of a regulatory element that is operably linked to a nucleic acid molecule that encodes a SPL polypeptide, wherein the regulatory element comprises a GATA transcription factor-binding motif.
 13. The method of claim 1 wherein the agent that alters sphingosine-1-phosphate lyase (SPL) activity is selected from the group consisting of (a) a mutated form of a nucleic acid molecule that encodes a SPL polypeptide wherein the mutated form encodes a dominant negative mutant SPL polypeptide, or a complementary polynucleotide thereto, and (b) a dominant negative mutant SPL polypeptide encoded by (a), wherein the nucleic acid molecule that encodes a SPL polypeptide is selected from the group consisting of (i) a nucleic acid molecule comprising a nucleotide sequence as set forth in SEQ ID NO:1 or a complementary sequence thereto, or as set forth in SEQ ID NO:3 or a complementary sequence thereto, (ii) a nucleic acid molecule comprising a nucleotide sequence that hybridizes under moderately stringent conditions to the nucleic acid molecule of (i) and that encodes a polypeptide having sphingosine-1-phosphate lyase (SPL) activity, and (iii) a nucleic acid molecule that encodes a SPL polypeptide which comprises an amino acid sequence as set forth in SEQ ID NO:2 or a portion of SEQ ID NO:2 having sphingosine-1-phosphate lyase (SPL) activity, or as set forth in SEQ ID NO:4 or a portion of SEQ ID NO:4 having sphingosine-1-phosphate lyase (SPL) activity. 